BiAnaCA

BiAnaCA: Tool Development for Calculation and Data Analysis of

BioAnalytes in Biochemical Assay Micro Plate Reader Method

BiAnaCA ~ 1.0
User Guide

Mr. Venkateswara Rao Amara

Mr. Sujit R. Tangadpalliwar

Ph.D. Scholar

&

Ph.D. Scholar
Dept. of Pharmacology

Dept. of Pharmacoinformatics

BiAnaCA

BiAnaCA

Index
About BiAnaCA
Introduction
BioAssay Protocol
Statistical Data analysis
Applications

HOW to Use?

Step 1: Data Entry

Step 2: Standard Calibration curve plot
Step 3: Calculation of Concentration
Step 4: Data Analysis
Step 5: Plot the Graphs
Step 6: Statistical Treatments
Step 7: Report Generation

Contact us

BiAnaCA
About us:

Department of Pharmacoinformatics, NIPER, S.A.S.Nagar is

engaged actively in developing various tools / software for
pharmaceutical sciences. Team BiAnaCA has developed tool for
biochemical assay analyzer and calculator. The developed tool will be
extremely

useful

for

the

Pharmacology,

Pharmaceutics,

Pharmaceutical Analysis, Biotechnology, PTBT and Natural Products

departments where, they are performing Biochemical assay

experiments frequently.

Introduction
Bio Chemical Assay of Bio Analytes:
An assay is an investigative (analytic) procedure in laboratory
medicine, pharmacology, environmental biology, continuous delivery,
and molecular biology for qualitatively assessing or quantitatively
measuring the presence or amount or the functional activity of a
target entity (the analyte).
Here, they are performing bio chemical assays of bio analytes
in animal models in Department of Pharmacology using Cuvettes or
96- Well Micro plate readers by Colorimetric or Spectrophotometric
analytical methods.
*Laboratory Information Management System (LIMS)

Biochemical Assay Protocol

Download and Installation

Download
the
BiAnaCA
for
your
system
http://www.niper.gov.in/pi_dev_tools/pi_toolsdev_main.htm

from

To run the BiAnaCA you just need java run time environment (JRE)
properly installed and updated as per your system configuration.

Download and update latest java JRE.

Download the zip folder and extract all files to a folder where you
want to install it. You can install it anywhere but Make sure that it has
included executable BiAnaCA_BetVersion.jar file and a lib folder with
demo folder inside lib folder. Do not move or Rename files within it.
Click on BiAnaCA_BetaVersion.jar to start the application.

You can find the tutorial, sample files and manuals in the folder
lib/demo/.

Applications
BiAnaCA can be used not just for biochemical assays but any assay
which involves spectrophotometric absorbance readings and you
want to calculate the unknown concentration from the standard
point or calibration curve method.
Can be used well for 96 well plate but it is not restricted to 96 well it
can be used for any number of large data set if you provide in the
proper .csv file format.
Can be used separately for linear regression curve analysis and
statistical analysis also for any other applications
Can generate .pdf reports by a software which can be help as
regulatory requirement and documentary evidence
It is totally free in nature and Fast, user friendly and efficient enough
for academic or industrial research
It is applicable not in just pharmacy or medical field but any clinical,
biotech, analytical chemistry, agriculture and science field

Layout of Work Flow

Experiment
Data upload

Perform the Experiments.

Fill the Project Details.
Upload the Reading Data.

Calculation
Data Analysis

Select Calculation method.

Perform Calculation.
Perform Statistical Analysis

Visualization
Result Reports

Plot the Graphs

Generate Reports

Home Screen

New Project: Fill the Experimental Details there in

Step 1: Fill the project and group details

Name of your this assay project
Name of person, date and all other reference detail which you want to print
in report fill them in the given boxes. You can copy paste with ctrl+c / ctrl+v
functions.
Then give the number of groups like control, treatment A, B , C etc. or groups
like formulation A, B, C or Group of compounds etc. excluding standard and
blank.
Tick the appropriate weather standard and/or blank were used or not.
Enter the number of groups and click enter.
Enter the number of replicas performed for each sample. E.g. 1 for single, 2
for duplicate and 3 for triplicate like wise. Click on OK Start.
Now enter the code of group and number of samples in each group. You can
use tab and arrow keys for the navigation purpose.
Click submit for further process to upload the reading data
or you can reset for new details.

4
3

Step 2:Upload the Reading data

Select the
method

File Upload *

.csv / .txt file

Sample code
and readings

Manual Entry

96 well
Plate reading

Fill the Readings

in opened
dialog box

*To view the sample files go to Lib//demo// TestData.csv, or TestData.txt, or Test_96WellData.csv

Select the options

browse and upload the file as per given format

Format of Data.csv file (Save as .CSV

coma separated value format from excel)

First row Titles

First column just
sample code
Samples in the
Sequence of
given group
Details
Save as .csv file
Template file
Available in folder
Lib\demo\data.csv

Format of Data.txt file (give tab -> to

separate values and enter for next sample)

Set the Outlier limit

You can check the outliers if any by setting the
limits in (%CV) % co-efficient of variation
between the replicate readings of same sample
By default set value is 10 % C.v.
It will just notify the outlier detection analysis in
message box.
If you want to edit you can edit the data in file
and re upload it or you can continue with
calculation.
Now Select the calculation method and proceed
further to calculate the unknown concentration.

Or if you want to upload 96 well plate reading file the Format is:
Enter the readings of Samples in the Sequence of given group Details
in A-H column 12 rows. And Save as .csv file
Template file Available in folder: Lib\demo\Test_96Welldata.csv

standard readings

Blank readings

For 96 well plate reading files click it

browse and upload the file as per given format

This is for manual entry option

after entering data you can save it also as a .csv file

Editable
Sample
codes

Few useful tricks for BiAnaCA users

If you selected third option and uploaded file with just 96 readings and missing
the sample codes then here is a trick for you to save and organize your file with
code.
First click this well icon to select 96 well plate file and then click upload file.
Select same one.
Now perform the calculation and on the next tab you may see concentrations
but no sample codes
So now come back to project detail tab and select the manual entry radio button
and you will find the table filled with both sample code and readings. Now click
ok submit and save the file if you wish.

Again just click on calculate button and your tables with sample code will be
updated.
Here one more safety trick is used to prevent the user enter the characters or
string in the some boxes where the number or integers are must so in that case
box will be hanged red until you enter in the proper format.
And anytime you need hint or help just have a look at message box it may give
you some suggestions for the next step
You can reset or restart the project in case if any strange mishap occurs

Calculation of Concentration
Option 1: from the single point standard concentration

Calculation of Concentration
Option 1: from the single point standard concentration
Enter the known standard concentration and their
mean absorbance reading
Give the Dilution factor of sample solutions if any or
else default value of dilution factor is 1
Give the units of standard and sample concentration to
be measured (sample concentrations will calculated in
same unit as of given standard concentrations)
Click on calculate button and find the results on the
screen in the next tabbed pane.
Beer-Lambert
law, A= abc

Conc(unk) = Conc(std) * Abs(unk) / Abs(std)

Calculation of Concentration
Option 2: From standard curve calibration and
regression analysis equation

Calculation of Concentration

Option 2: From standard curve calibration and regression analysis equation

Give the Dilution factor of sample solutions if any dilution performed or else
default value of dilution factor is 1 (No extra Dilution)
Give the units of standard and sample concentration to be measured (sample
concentrations will calculated in same unit as of given standard concentrations)
Enter the number of sample or points in the calibration curve, click the enter and
in the side box that many cells will appear for concentration and corresponding
readings
Fill the data and click the Plot Equation, find the result in message box and
graphical plot is generated in the last tab of calibration curve plot, view it.
You can view, edit, print, copy or save the plot in different formats from its
properties option by right click on the plot.
Linear regression equation Y =mx + c is generated
slope, intercept and coefficient R square value ( near to 1 is more linear)
Come back to Project detail screen and Now Click on activated calculate button
and find the results on the screen in the next tabbed pane.

Regression equation : Y= MX+C

Conc = (abs-intercept)/slope

(Abs = slope*Conc + intercept)

Multiplies it with Dilution factors.

Standard Calibration curve plot

Plot the Equation and Click on Calculate

Result data sheet for sample wise

concentration calculation

Group wise Data Analysis

Click on Plot Opens this tab

Click on the plot and explore the

properties, edit, view or save plots

Perform the statistical Tests

Select the tests, groups, parameters and perform

Statistical Analysis Tests

Select your test first:

Students T test (Unpaired)( for equal variance)

Students T test (Paired)
Unpaired T Test (Welch correction) (unequal variance)
One Sample T Test
One Way Anova
Column Statistics
F test (Variance Ratio)

Select alpha value from List

0.05 (95% Confidence interval)

0.01 (99% Confidence interval)
0.001 (99.9% Confidence interval)
0.1 (90% Confidence interval)

Select P-Value test

One Tail test
Two tail test

Selection of Statistical Tests

Number of
Groups
Other tests
More Groups
comparison

Two Group
comparison

Paired T-test
*Both groups
Must have
same sample size
For paired comparison

One sample
t-Test

Unpaired t-Test
One way
ANOVA
Equal
Variance
* Most widely
Used for
bioassay cases
If sample sizes
are not same

Unequal
variance
*Uses the
Welch Correction
factor

F-Test

Column
Statistics

To perform Student T-tet or other t-Tests analysis

Select two Groups, alpha value, one or two tail and Click perform

In Result table you can find sample size, mean +- SEM, P value,
T Statistic, Significance, Null Hypothesis rejection, deg. of freedom etc.

To perform One Way Anova analysis test

Select Groups, alpha value, one or two tail test and Click perform

View the ANOVA Results, Click on Print Report to generate it

Report and Result files are generated in a folder dedicated to

project name and it will open up directly on your screen

About Tool and team BiAnaCA. Click and Contact us.

Help: Quick Guide and Demo

Demo will run a flash html tutorial* in your browser ( only if you have downloaded it during installation)

Dear User,